Daily challenges in the lab

Ah, such is the life of a scientist, where nothing, nothing is straightforward!  Science never sleeps; it is like a never-ending unfolding story, with as many twists and turns as you like and then some.  Recently, yours truly has been going through a rough patch in the lab of late: a ligation experiment that would allow for some wonderful and intriguing discoveries isn't working, the mutant yeast strains I have generated are not what they seem.  I am repeating some stages in my experiment that I did three months ago.  In the meantime, other experiments I really want to do to get things moving are on hold while I try to find out what I am actually working with.

What the hell are you?! Answer me, damn mutant!!

 If molecular biology was a video game and there were bosses - gigantic monsterous enemies you must battle to get to the next stage (not your supervisor, although opinions may differ on this point) - then ligation would definetly be one big bad boss!  The idea of cutting up pieces of DNA with restriction enzymes and sticking them together with DNA ligase sounds simple enough, but there is a lot of fine tuning involved.  The ratio of vector DNA versus insert DNA is important, get this wrong and it might not work.  The ATP in the ligase buffer needs to be in good condition as this is needed by the enzyme to function.  The temperature needs to be right, the salt and pH conditions need to be right, your mood needs to be right, the funny dance that you do with the pirouette at the end to ward off bad luck...right! 

Giant, evil-looking ligation boss: 1 million points ; tiny, suffering scientist: none

But for now, something is amiss and I need to find out why so I can move on.  One of the frustrating things about science is time: it takes a good few hours to digest the DNA, half an hour to clean it up, half an hour to prepare it for ligation and then another hour for the actual reaction.  It can be so frustrating to find out after all that time it hasn't worked and you have used up loads of enzyme, tons of DNA and it is late in the day so there is little you can do about it - apart from huff and puff all the way home.

So, good people of the blogosphere, if there are any scientists out there who can impart a little advice on how to make ligations work, please feel free to sprinkle me some crumbs of wisdom.  Otherwise just wish me luck - I sure could do with some!   

Scientists selling their wares in a time of crisis

Escherichia coli under the microscope (Image by Rocky Mountain Laboratories, NIAID, NIH)

The big news for the best part of a week has been the E. coli outbreak in Northern Germany, and this morning Professor John Oxford, a leading expert in virology and chairman of the Hygiene Council was interviewed by Eamonn Holmes on his views of the outbreak and what advice he could give to the general public to keep themselves safe.


The Professor answered with a brief low-down of where E.coli comes from ( the animal and human gut) how it got from there to the vegetables (animal and sometimes human waste is used to make manure that is used to fertilise crops) and why, in this case, that the E. coli bacteria from the manure has managed to make it into people's mouths (this new mutant strain of E. coli is more "sticky" causing it to stick to the outside of vegetables so that conventional washing is not enough to remove it.  It also has a way of being able to "wriggle" into the vegetable - where no amount of washing has an effect).  All of these points I agree with - the first two points are common knowledge and the E. coli strain (Enterohemorrhagic E.coli ) uses bacterial fimbriae to attach to surfaces, therefore making it sticky.  The "wriggle" bit I am not too sure about as that would suggest the bacteria has a "tail" that would allow for movement.  However, manure is sprayed on to crops and you would imagine that the fertiliser - and the bacteria - is capable of getting into the little crevices and gaps present in the natural shape of the vegetable.

 The shape of the vegetable, the fruit and their leaves makes it harder to remove potential pathogens (Image by User: Geographer)

However, when it came to giving advice on how to keep ourselves safe from getting infected, the Professor seemed to go off subject and talked about personal hygiene, handwashing and how "manners" is important to make sure that others are kept safe from infection by our own actions.  That is all very well and good and I agree one hundred percent - one should wash hands regularly and yes, one should be considerate towards others, like having your hand over your mouth when sneezing or coughing - but how does that relate when it is the foodstuff that is contaminated? How is handwashing and manners going to make the bacteria unstick from your raw vegetables and stop it from entering your stomach?

  If I scrub my hands hard enough, the bacteria from my salad will disappear! (Image by Serenity)

It was the next words that revealed what was behind his statement - I can't remember the exact words but the word "Dettol" was used.  Bear in mind that John Oxford had some involvement in the Dettol Habit survey and that the Hygiene Council is sponsored by Reckitt Benckiser, a multinational corporation that counts Dettol as one of its power brands.  The Professor continued and ended the interview with advice that people should disinfect more.

 The word infomercial comes to mind

It is already bad enough that in cases of disease outbreaks that we, the general public, have little information to go on except that conveyed by the media - information that is usually sensational and serves to promote fear and panick.  Now there are professionals, experts in the field, that are using this hysteria as an opportunity to endorse products and increase their project funding. 

In times of crisis we all look to those with more knowledge and expertise than us to inform and guide us and we hope that their information is in our best interests.  What we don't need is for these people to take advantage of the situation for their own.  What the good Professor should have said is that since the bacteria cannot be easily removed from the raw vegetables or fruits by washing, that they be cooked thoroughly instead before consumption.  This is just common sense and doesn't require a council and doesn't require a study.

It certainly doesn't require product promotion!

Source: Sky news

Also see: Sell it to me!        

  

Queen Victoria on film!!!

So there I was, measuring the intensity of the radiation emitting from my southern blot. The click, click, click-click-click sounds from the geiger counter sounded a bit too frequent (meaning that the blot is not as clean as it should be and needs extra washing to get rid of the residue isotope) but that day I was impatient (and a bit desperate!) to see something, anything on my blot. So I carefully dried it on a piece of tissue, wrapped it in cling film, stuck it down in the casette and exposed it to film overnight.

I had expected to see bands on the film of my DNA with some residue blobs here and there. Imagine the shock when I saw this! :

Over-exposure!! At its finest!!!

But look at the outline in the centre. Does it look familiar?

Queen Victoria! On MY film! How cool is that???

We are human after all

While trawling the internet, I found this story: 'American biologist trapped on UK beach phones 911... and is rescued after operators in Washington put her through to British police.' Not the finest moment for anyone and especially for one whose profession portrays them to be intelligent and knowledgeable. However, we must remember a job title is just a job title and a qualification is just a qualification. Underneath it all there is a person, who can make silly mistakes just like everyone else. We are human after all.

Lab frustrations!!!

From practical grievances to writing up and publishing the damn stuff, these links say it all!


Caught in a bad project!


Herr Professor is not amused...

All this leads to everyone submitting their work to this prestigious journal:

Where all submissions, regardless of the quality, will be... rejected! Here are the reasons for why this is a good thing as according to the journal:

1. You can send your manuscript here without suffering waves of anxiety regarding the eventual fate of your submission. You know with 100% certainty that it will not be accepted for publication.

2. There are no page-fees.

3. You may claim to have submitted to the most prestigious journal (judged by acceptance rate).

4. The JofUR is one-of-a-kind. Merely submitting work to it may be considered a badge of honor.

5. You retain complete rights to your work, and are free to resubmit to other journals even before our review process is complete.

6. Decisions are often (though not always) rendered within hours of submission.


Have a nice day and keep smiling!

Check out: Journal of Universal Rejection

I'm cooking on sunshine! (Wooah!)

The concept of green energy becoming a perceivable substitute for coal and gas was validated again - this time in the kitchen. World-acclaimed Catalan designer Martí Guixé, Finnish food visionary Antto Melasniemi and Lapin Kulta beer have joined forces to present the Lapin Kulta Solar Kitchen Restaurant, where all the cooking is done and powered only by pure solar energy.

According to the official website, the Lapin Kulta Solar Kitchen Restaurant "highlights key contemporary themes: a nature-driven process, flexibility and immediacy. Depending on the sunshine of a given day, the kitchen is able to do a solar barbecue, meals prepared at lower temperatures or salads. The restaurant will therefore also test people’s flexibility: if it rains, we have to adapt, reschedule and deal with the nature-dependent delays. Immediacy will be evident in the urgency of movements and decisions, and real-time information: a cloud could change the course of a business lunch!"

Unlike the traditional way of cooking, solar heat affects the taste and texture of the dish in a surprising and positive way, producing a completely different taste experience

- Antto Melasniemi and Martí Guixé

Last month, their solar cooking project showcased at Milan Design Week 2011. This summer the restaurant will be setting up all over Europe, with the project making a trail towards the never-setting summer sun of the Arctic Circle. Customers can marvel at this creative and innovative use of the sun while enjoying gourmet cooking, beer, life and art.

Check out their website to see if they are coming to a city near you. Once you have found this out and you want to know when they are opening, look up to the sky...

Source: Lapin Kulta Solar Kitchen Restaurant

Biocouture

How cool is this - Suzanne Lee of Biocouture at Central Saint Martins has established a method to produce material that can be molded into clothing - a method that involves growing bacteria on sweetened green tea in bathtubs!

A biofilm being grown on sweet green tea. Picture courtesy of Biocouture





The bacteria feeds on the sweet tea and grow and aggregate to form biofilms on the surface of the liquid. The cellulose that is being produced by the bacteria (and what holds the biofilm together as a matrix) can be taken after it has grown to a thickness of around 1.5 cm, dried out and molded into clothes. These can be dyed a variety of colours, the quantity of which is needed being less than that for other commercially used materials, an added benefit for the environment.

A Biobiker jacket. Picture courtesy of Biocouture


The Biocouture material is described as having a "vegetable leather" feel. Like vegetable waste when unwanted it can be discarded and treated as compost.

At a time when we are looking for green solutions for various industries, this novel method seems beautifully simple and has a fantastic result. The question remains whether this unique material can be made strong enough for everyday wear-and-tear, can be made water resistant and whether a variety of materials can be made to substitute for the likes of denim or nylon. At present Suzanne Lee, a Technology Entertainment and Design (TED) fellow and her team are planning to scale up this whole process that will hopefully involve the use of waste streams from the food and drink industry. A Stella dress to go with a Mac-mac and a cola clutch bag? I am excited!!! :D

I wish this project the best of luck. I will be looking forward to buying a handbag from them in the not-too distant future! ;)

Source: Biocouture

See also:

Suzanne Lee - a profile
Central Saint Martins College of Art and Design
London Science Museum: Trash Fashion
TED Fellowship

Chernobyl: 25 years on

A sarcophagus in the Chernobyl Zone. Image by Piotr Andryszczak

26th of April was the 25th anniversary of the Chernobyl disaster. The Presidents of Russia and Ukraine attended a commemoration ceremony at the site of the world's worst nuclear disaster and were united in calls for new international ruling to ensure the safe running and development of nuclear facilities.

The explosion and fire at the Chernobyl facility based in the former USSR released massive quantities of radioactive material into the surrounding area and into the atmosphere, where it was detected as far away as Norway and Scandinavia. To this day, the areas most effected by the nuclear fallout are still dealing with its aftermath - large areas of Belarus, Ukraine and Russia are still contaminated with heavy radioactive elements. Death and poor health attributed to high radiation exposure are still being reported.

Chernobyl radiation map from CIA handbook


President Dmitry Medvedev did not specify what proposals he would bring to the international community. He did, however, stress that the Chernobyl disaster has taught that truth and honesty is paramount to protecting lives: "it is duty of the state to tell the truth to its people. It must be acknowledged that the (Soviet) state did not always behave correctly".

However, lessons from the present-day disaster at the Fukushima nuclear plant must also be recognised. Here, the incident was not a man-made accident like Chernobyl but caused by the uncontrollable and unanticipated force of nature. To save lives, one needs to know at an instant the extent and the immediate consequences of the damage to the facility and the impending nuclear fallout in order to take effective action - knowledge that could not have been apprehended fast enough for the officials in Japan to make any formal statements. It is here that honesty and truthfulness, under a massive plume of radioactive dust, do not appear to hold much value.

A word that does appear to be of value is conscience. What we know from both these major incidents is the sheer magnitude of the danger that a nuclear fallout poses to life and health; a danger that cannot be naturally sensed or outrun, that can be so easily caused by man or nature and that is irreversible, destructive and long lasting. One must question whether our demand for energy outweighs the value of human life and the value of our environment - one that in future will be serving as a massive dumping ground for nuclear waste.

Safer, renewable and clean energy technology exists. Now would be the perfect time for world leaders to listen to their conscience, and their people, and make a move away from the tempting toxicity that is nuclear power. What should be the real take-home message from Chernobyl and Fukushima is: haven't we seen enough?

Source: Reuters

Also see:

Channel 4 4od: Nuclear Eternity

Heavy Water: A film for Chernobyl

RNase Evil

For those scientists working with RNA you will feel my pain: so I got in early today to set up an RNA glyoxal gel:

I loaded my RNA samples, ran the gel for 5 hours and this was the result:

Arrraagh!!!!!!

It appears that I have RNase contamination in my gel! This is an enzyme found in abundance on skin (and in saliva and tears) that specifically destroy RNA, hence the horrible smeary bands you see. RNase can be found on almost every surface in physical contact and is hell to get rid of. For a better description - and for how I and many others who work with RNA feel about this enzyme - check out this page or just take me at my word - Evil! Evil! Evil!

Imagine you are the RNA, and those are RNases...coming after you...


RNA stands for ribonucleic acid and is one of three types of macromolecule (the other two being DNA and protein) that are essential for all forms of life. RNA is very similar to DNA in that it is made up of a string of nucleotides, the sequence of which allows RNA to encode genetic information, similar and as derived from DNA. However, unlike DNA, different types of RNA molecule exist, and are involved in many enzymatic processes within the living cell: that as well as encoding and passing on the information to synthesise proteins, RNA can direct and regulate gene expression, function in protein synthesis and sense and respond to cellular signals.

An x-ray structure of transfer RNA - a type of RNA that is involved in recruiting and linking amino acids together in the process of protein synethesis. Image by Yikrazuul.



Yet despite being so deeply involved in many vital biological processes RNA is very unstable. This is not surprising since a lot of these processes are rapidly occurring and are responsive to internal and external factors. RNA molecules generated now may not appropriate for what may occur at a later stage; their prolonged presence may even be deterimental to the cell in that specific catalytic processes may be overexpressed or suppressed; certain functions may be deregulated. One can say instead of being cogs in a well oiled machine they are now like spanners in the works.

So, yes, it is good that RNA is easily degradable and RNase is in abundance to do it - just not when one is trying to isolate and study it!!! So it will be take-two tomorrow: I am going to encase my hands in chain-mail gloves and treat all my equipment and my bench with a flame thrower. Hasta la vista RNase...


Kidding!!!


Wish me luck!

Of Science and Religion

Depiction of Jesus Christ on stained glass. Image by Toby Hudson

While enjoying the Easter holidays I came across this article in the New Statesman where the author, Andrew Zak Williams, interviewed a variety of leading public figures and scientists on their views on Christian faith and their reasons for believing. The responses are diverse as they are fascinating - Religious leaders James Jones and Richard Chartres describe the Christian faith as unquestionable. Others such as the barrister Cherie Blair, journalist Jeremy Vine and former Conservative minister Jonathan Aitken see religion as natural and a form of solace, something that cannot be explained. The British author Peter Hitchens and Professor of Psychology David Myers find that faith provides a guide and a meaning to life, that it holds the key to the many questions of the universe and of our existence.

It is perceived that the scientist's view is a little more divorced than those expressed and in this article it shows - Quantum Physicist Paul Davies prefers "useful concepts" than belief; that the word 'God' is undefined and idea of a spiritual entity capable of thought and control is unacceptable. Theoretical physicist Peter Richmond goes further, stating that although the teachings of the Bible are still relevant to this day, the scriptures should not be taken literally. However, the likes of Professor of biology Kenneth Miller, astrophysicist Hugh Ross and Professor of climate change Mike Hulme confirm a personal belief in the Bible and in God; a belief that stems from, surprisingly, scientific findings, scientific rationality and scientific values.

There is a concept perpetuated in the UK media that science is very much against religion - that it is God versus Nature; creationism versus evolution. However, from these short interviews it can be seen that the lines are blurred - that there are well respected and successful scientists who openly embrace religion and the concept that scientific methodology is not appropriate to explain or define faith.

Source: New Statesman